Seleção genômica para características longitudinais de bovinos da raça Holandesa

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Prevalence of chronic rhinosinusitis in Sao Paulo

Introduction: Studies designed to investigate chronic rhinosinusitis (CRS) epidemiology play an important role to assess population's distribution and risk factors to result in the development and promotion of public health policies. Method: This study design is a survey carried out with a complex two-stage cluster sampling plan. Personal interviews were carried out with 2,003 individuals. The questionnaire included the epidemiological criteria for CRS. Demographic data, history of physician-diagnosed respiratory diseases (asthma, sinusitis, rhinitis), smoking, family income, educational attainment, and household characteristics were also evaluated. Results: The overall response rate was 93.9% of the households. Mean age was 39.8 +/- 21 years; 45.33% were male. The overall prevalence of CRS in the city of Sao Paulo was 5.51%. We found a significant association between diagnosis of CRS and diagnosis of asthma and CRS and diagnosis of rhinitis and a significant association between presence of CRS and belonging to the low-income subgroup. Conclusion: The municipality of Sao Paulo has an urban population of 11 million. According to the present study, the prevalence of CRS is 5.51%, which represents more than 500,000 individuals affected by this condition in the city.

Quedas em idosos e sua relação com a capacidade funcional

OBJETIVO: determinar a prevalência de quedas em idosos e sua relação com a capacidade funcional. MÉTODO: trata-se de estudo epidemiológico transversal de base populacional, com uma amostra por conglomerado de duplo estágio de 240 sujeitos, com idade acima de 60 anos, de ambos os sexos, residentes em Ribeirão Preto, SP. Os dados foram coletados entre novembro de 2010 e fevereiro de 2011 e utilizaram-se os questionários: perfil social, avaliação de quedas, Medida de Independência Funcional e Escala de Lawton e Brody. Foi adotado o nível de significância de 0,05. Para a identificação da ocorrência das quedas e sua relação com a capacidade funcional, foram utilizadas razão de prevalência e de chances de prevalência e regressão logística múltipla. RESULTADOS: a média de idade foi de 73,5 anos (±8,4), 25% com 80 anos ou mais, predomínio do sexo feminino; 48,8% estudaram de 1 a 4 anos. Média de 1,33 quedas (±0,472); com maior prevalência em mulheres e idosos mais jovens; o local mais frequente foi o quintal e o banheiro. Houve forte correlação entre o nível de independência funcional e as atividades instrumentais com a idade, e não houve relação entre os idosos que sofreram queda e as variáveis sexo e idade. CONCLUSÃO: houve predomínio de mulheres que sofreram quedas relacionadas à independência funcional, podendo-se prevenir com estratégias de promoção à saúde ao idoso, política essa para oferecer condição de vida à pessoa no processo de envelhecer.

Detection of Hepatitis B virus subgenotype A1 in a Quilombo community from Maranhão, Brazil

Abstract Background The Brazilian population is mainly descendant from European colonizers, Africans and Native Americans. Some Afro-descendants lived in small isolated communities since the slavery period. The epidemiological status of HBV infection in Quilombos communities from northeast of Brazil remains unknown. The aim of this study was to characterize the HBV genotypes circulating inside a Quilombo isolated community from Maranhão State, Brazil. Methods Seventy-two samples from Frechal Quilombo community at Maranhão were collected. All serum samples were screened by enzyme-linked immunosorbent assays for the presence of hepatitis B surface antigen (HBsAg). HBsAg positive samples were submitted to DNA extraction and a fragment of 1306 bp partially comprising HBsAg and polymerase coding regions (S/POL) was amplified by nested PCR and its nucleotide sequence was determined. Viral isolates were genotyped by phylogenetic analysis using reference sequences from each genotype obtained from GenBank (n = 320). Sequences were aligned using Muscle software and edited in the SE-AL software. Bayesian phylogenetic analyses were conducted using Markov Chain Monte Carlo (MCMC) method to obtain the MCC tree using BEAST v.1.5.3. Results Of the 72 individuals, 9 (12.5%) were HBsAg-positive and 4 of them were successfully sequenced for the 1306 bp fragment. All these samples were genotype A1 and grouped together with other sequences reported from Brazil. Conclusions The present study represents the first report on the HBV genotypes characterization of this community in the Maranhão state in Brazil where a high HBsAg frequency was found. In this study, we reported a high frequency of HBV infection and the exclusive presence of subgenotype A1 in an Afro-descendent community in the Maranhão State, Brazil.

Fe valence fluctuations and magnetoelastic coupling in Pb-based multiferroics perovskites

Lead-based multiferroics perovskites with nominal compositions Pb(Fe1/2Nb1/2)O3 and Pb(Fe2/3W1/3)O3 were synthesized following a two-stage method. Magnetic proprieties were investigated and correlated to anelastic proprieties, measured by the conventional pulse-echo method. The discussions are focused in the region around 250 K, where magnetoelectroelastic instabilities have been observed. X-ray absorption nearedge structure (XANES) study further indicates that the edge position varies with temperature revealing a fluctuation on the valence of iron ions with the temperature, which can be related to a variation in anelastic and magnetic proprieties.

Simple and objective method for routine detection of the macular pigment xanthophyll

A new simple method for two-dimensional determination of optical density of macular pigment xanthophyll (ODx) in clinical routine is based on a single blue-reflection fundus image. Individual different vignetting is corrected by a shading function. For its construction, nodes are automatically found in structureless image regions. The influence of stray light in elderly crystalline lenses is compensated by a correction function that depends on age. The reproducibility of parameters in a one-wavelength reflection method determined for three subjects (47, 61, and 78 years old) was: maxODx = 6.3%, meanODx = 4.6%, volume = 6%, and area = 6% already before stray-light correction. ODx was comparable in pseudophakic and in an eye with a crystalline lens of the same 11 subjects after stray-light correction. Significant correlation in ODx was found between the one-wavelength reflection method and the two-wavelength autofluorescence method for pseudophakic and cataract eyes of 19 patients suffering from dry age-related macular degeneration (AMD) (R(2) = 0.855). In pseudophakic eyes, maxODx was significantly lower for dry AMD (n = 45) (ODx = 0.491±0.102 ODU) than in eyes with healthy fundus (n = 22) (ODx = 0.615±0.103 ODU) (p = 0.000033). Also in eyes with crystalline lens, maxODx was lower in AMD (n = 125) (ODx = 0.610±0.093 ODU) than in healthy subjects (n = 45) (ODx = 0.674±0.098 ODU) (p = 0.00019). No dependence on age was found in the pseudophakic eyes both of healthy subjects and AMD patients.

Genetic association studies under the population stratification, family pedigree and application to genome-wide association studies

This dissertation has three separate parts: the first part deals with the general pedigree association testing incorporating continuous covariates; the second part deals with the association tests under population stratification using the conditional likelihood tests; the third part deals with the genome-wide association studies based on the real rheumatoid arthritis (RA) disease data sets from Genetic Analysis Workshop 16 (GAW16) problem 1. Many statistical tests are developed to test the linkage and association using either case-control status or phenotype covariates for family data structure, separately. Those univariate analyses might not use all the information coming from the family members in practical studies. On the other hand, the human complex disease do not have a clear inheritance pattern, there might exist the gene interactions or act independently. In part I, the new proposed approach MPDT is focused on how to use both the case control information as well as the phenotype covariates. This approach can be applied to detect multiple marker effects. Based on the two existing popular statistics in family studies for case-control and quantitative traits respectively, the new approach could be used in the simple family structure data set as well as general pedigree structure. The combined statistics are calculated using the two statistics; A permutation procedure is applied for assessing the p-value with adjustment from the Bonferroni for the multiple markers. We use simulation studies to evaluate the type I error rates and the powers of the proposed approach. Our results show that the combined test using both case-control information and phenotype covariates not only has the correct type I error rates but also is more powerful than the other existing methods. For multiple marker interactions, our proposed method is also very powerful. Selective genotyping is an economical strategy in detecting and mapping quantitative trait loci in the genetic dissection of complex disease. When the samples arise from different ethnic groups or an admixture population, all the existing selective genotyping methods may result in spurious association due to different ancestry distributions. The problem can be more serious when the sample size is large, a general requirement to obtain sufficient power to detect modest genetic effects for most complex traits. In part II, I describe a useful strategy in selective genotyping while population stratification is present. Our procedure used a principal component based approach to eliminate any effect of population stratification. The paper evaluates the performance of our procedure using both simulated data from an early study data sets and also the HapMap data sets in a variety of population admixture models generated from empirical data. There are one binary trait and two continuous traits in the rheumatoid arthritis dataset of Problem 1 in the Genetic Analysis Workshop 16 (GAW16): RA status, AntiCCP and IgM. To allow multiple traits, we suggest a set of SNP-level F statistics by the concept of multiple-correlation to measure the genetic association between multiple trait values and SNP-specific genotypic scores and obtain their null distributions. Hereby, we perform 6 genome-wide association analyses using the novel one- and two-stage approaches which are based on single, double and triple traits. Incorporating all these 6 analyses, we successfully validate the SNPs which have been identified to be responsible for rheumatoid arthritis in the literature and detect more disease susceptibility SNPs for follow-up studies in the future. Except for chromosome 13 and 18, each of the others is found to harbour susceptible genetic regions for rheumatoid arthritis or related diseases, i.e., lupus erythematosus. This topic is discussed in part III.

STATISTICAL METHODS FOR RARE AND COMMON VARIANT ASSOCIATION STUDIES

Complex human diseases are a major challenge for biological research. The goal of my research is to develop effective methods for biostatistics in order to create more opportunities for the prevention and cure of human diseases. This dissertation proposes statistical technologies that have the ability of being adapted to sequencing data in family-based designs, and that account for joint effects as well as gene-gene and gene-environment interactions in the GWA studies. The framework includes statistical methods for rare and common variant association studies. Although next-generation DNA sequencing technologies have made rare variant association studies feasible, the development of powerful statistical methods for rare variant association studies is still underway. Chapter 2 demonstrates two adaptive weighting methods for rare variant association studies based on family data for quantitative traits. The results show that both proposed methods are robust to population stratification, robust to the direction and magnitude of the effects of causal variants, and more powerful than the methods using weights suggested by Madsen and Browning [2009]. In Chapter 3, I extended the previously proposed test for Testing the effect of an Optimally Weighted combination of variants (TOW) [Sha et al., 2012] for unrelated individuals to TOW &ndash F, TOW for Family &ndash based design. Simulation results show that TOW &ndash F can control for population stratification in wide range of population structures including spatially structured populations, is robust to the directions of effect of causal variants, and is relatively robust to percentage of neutral variants. In GWA studies, this dissertation consists of a two &ndash locus joint effect analysis and a two-stage approach accounting for gene &ndash gene and gene &ndash environment interaction. Chapter 4 proposes a novel two &ndash stage approach, which is promising to identify joint effects, especially for monotonic models. The proposed approach outperforms a single &ndash marker method and a regular two &ndash stage analysis based on the two &ndash locus genotypic test. In Chapter 5, I proposed a gene &ndash based two &ndash stage approach to identify gene &ndash gene and gene &ndash environment interactions in GWA studies which can include rare variants. The two &ndash stage approach is applied to the GAW 17 dataset to identify the interaction between KDR gene and smoking status.

Evaluation of a Bayesian MCMC Random Effects Inference Methodology for Capture-Mark-Recapture Data

Monte Carlo simulation was used to evaluate properties of a simple Bayesian MCMC analysis of the random effects model for single group Cormack-Jolly-Seber capture-recapture data. The MCMC method is applied to the model via a logit link, so parameters p, S are on a logit scale, where logit(S) is assumed to have, and is generated from, a normal distribution with mean μ and variance σ2 . Marginal prior distributions on logit(p) and μ were independent normal with mean zero and standard deviation 1.75 for logit(p) and 100 for μ ; hence minimally informative. Marginal prior distribution on σ2 was placed on τ2=1/σ2 as a gamma distribution with α=β=0.001 . The study design has 432 points spread over 5 factors: occasions (t) , new releases per occasion (u), p, μ , and σ . At each design point 100 independent trials were completed (hence 43,200 trials in total), each with sample size n=10,000 from the parameter posterior distribution. At 128 of these design points comparisons are made to previously reported results from a method of moments procedure. We looked at properties of point and interval inference on μ , and σ based on the posterior mean, median, and mode and equal-tailed 95% credibility interval. Bayesian inference did very well for the parameter μ , but under the conditions used here, MCMC inference performance for σ was mixed: poor for sparse data (i.e., only 7 occasions) or σ=0 , but good when there were sufficient data and not small σ .

Proceedings of the Seventh Annual Biochemical Engineering Symposium

This is the seventh in a series of symposia devoted to talks by students on their biochemical engineering research. The first four meetings were held alternately at Kansas State University and the University of Nebraska–Lincoln, with participants from those two schools. The next two took place at Kansas State and then in conjunction with the 8lst American Institute of Chemical Engineers National Meeting in Kansas City, with attendees from Kansas State and Iowa State Universities. This meeting, at Iowa State, was the first to include participation from the University of Missouri–Columbia. Contents"Properties of Soluble and In:anoblized Dextransucrase," Hossein Kaboli and Yah Eric Chen, Iowa State University "Growth of Lipid-Producing Organisms on Formic and Acetic Acid-Containing Waste Waters," Lin-Chang Chiang, University of Missouri–Columbia "Design of an Automated Alkaline Copper Reducing Sugar Assay," Alfred R. Fratzke and James R. Frederick, Iowa State University "Determination of Oxygen Transfer Coefficients in Hydrocarbon Fermentations Using a Material Balance Method," Sarafin N. Sanchez and J. R. Gutierrez, Kansas State University "Oxygen Transfer Characteristics in One Stage and Two Stage Air-Lift Towers," Mark E. Orazem, Kansas State University "A Comparison of Biological Digestibility Tests for Cellulose," Dou-Houng Hwang, University of Missouri–Columbia "Mechanism of Enzymatic Hydrolysis of Cellulose," L. T. Fan, Yong-Hyun Lee, and Liang-Shih Fan, Kansas State University "Purification of Xylan-Hydrolyzing Enzymes," James R. Frederick, Alfred R. Fratzke, and Mary M. Frederick, Iowa State University "Cellulase Production from Bagasse and Pith," A. Ferrer, Y. Alroy, and I. Brito, Kansas State University

Gender-Fair language and professional self-reference: The case of female psychologists in Polish

The struggle to achieve gender equality is accompanied by efforts to introduce gender-fair language. In languages with grammatical gender this implies the use of gender-appropriate forms (feminine for women and masculine for males). In the present research, results of a mixed method approach—a corpus analysis, a survey, and an experiment—provide consistent evidence that in Polish, feminine forms are still infrequent in women’s self-reference and that women psychologists continue to use masculine titles. Moreover, a qualitative inquiry examines the reasons why women prefer masculine over feminine job titles. Integrating findings from the two-stage design, we are able to identify the obstacles to promoting social change with the help of language and to understand the reasons behind them.

The Nelaton Catheter Guard for Safe and Effective Placement of Subdural Drain for Two-Burr-Hole Trephination in Chronic Subdural Hematoma: A Technical Note

BACKGROUND For chronic subdural hematoma, placement of a Blake drain with a two-burr-hole craniotomy is often preferred. However, the placement of such drains carries the risk of penetrating the brain surface or damaging superficial venous structures. OBJECTIVE To describe the use of a Nelaton catheter for the placement of a subdural drain in two-burr-hole trephination for chronic subdural hematoma. METHOD A Nelaton catheter was used to guide placement of a Blake drain into the subdural hematoma cavity and provide irrigation of the hematoma cavity. With the two-burr-hole method, the Nelaton catheter could be removed easily via the frontal burr hole after the Blake drain was in place. RESULTS We used the Nelaton catheters in many surgical procedures and found it a safe and easy technique. This method allows the surgeon to safely direct the catheter into the correct position in the subdural space. CONCLUSIONS This tool has two advantages. First, the use of a small and flexible Nelaton catheter is a safe method for irrigation of a chronic subdural hematoma cavity. Second, in comparison with insertion of subdural drainage alone through a burr hole, the placement of the Nelaton catheter in subdural space is easier and the risk of damaging relevant structures such as cortical tissue or bridging veins is lower. Thus this technique may help to avoid complications when placing a subdural drain.

Bayesian dual threshold design with Dirichlet distribution: An alternative way to frequentist multi-stage phase II designs in oncology

Many phase II clinical studies in oncology use two-stage frequentist design such as Simon's optimal design. However, they have a common logistical problem regarding the patient accrual at the interim. Strictly speaking, patient accrual at the end of the first stage may have to be suspended until all patients have events, success or failure. For example, when the study endpoint is six-month progression free survival, patient accrual has to be stopped until all outcomes from stage I is observed. However, study investigators may have concern when accrual is suspended after the first stage due to the loss of accrual momentum during this hiatus. We propose a two-stage phase II design that resolves the patient accrual problem due to an interim analysis, and it can be used as an alternative way to frequentist two-stage phase II studies in oncology. ^

Bayesian adaptive designs for drug combinations in early phase clinical trials

Treating patients with combined agents is a growing trend in cancer clinical trials. Evaluating the synergism of multiple drugs is often the primary motivation for such drug-combination studies. Focusing on the drug combination study in the early phase clinical trials, our research is composed of three parts: (1) We conduct a comprehensive comparison of four dose-finding designs in the two-dimensional toxicity probability space and propose using the Bayesian model averaging method to overcome the arbitrariness of the model specification and enhance the robustness of the design; (2) Motivated by a recent drug-combination trial at MD Anderson Cancer Center with a continuous-dose standard of care agent and a discrete-dose investigational agent, we propose a two-stage Bayesian adaptive dose-finding design based on an extended continual reassessment method; (3) By combining phase I and phase II clinical trials, we propose an extension of a single agent dose-finding design. We model the time-to-event toxicity and efficacy to direct dose finding in two-dimensional drug-combination studies. We conduct extensive simulation studies to examine the operating characteristics of the aforementioned designs and demonstrate the designs' good performances in various practical scenarios.^

Adaptive clinical trial design for targeted therapy development

The development of targeted therapy involve many challenges. Our study will address some of the key issues involved in biomarker identification and clinical trial design. In our study, we propose two biomarker selection methods, and then apply them in two different clinical trial designs for targeted therapy development. In particular, we propose a Bayesian two-step lasso procedure for biomarker selection in the proportional hazards model in Chapter 2. In the first step of this strategy, we use the Bayesian group lasso to identify the important marker groups, wherein each group contains the main effect of a single marker and its interactions with treatments. In the second step, we zoom in to select each individual marker and the interactions between markers and treatments in order to identify prognostic or predictive markers using the Bayesian adaptive lasso. In Chapter 3, we propose a Bayesian two-stage adaptive design for targeted therapy development while implementing the variable selection method given in Chapter 2. In Chapter 4, we proposed an alternate frequentist adaptive randomization strategy for situations where a large number of biomarkers need to be incorporated in the study design. We also propose a new adaptive randomization rule, which takes into account the variations associated with the point estimates of survival times. In all of our designs, we seek to identify the key markers that are either prognostic or predictive with respect to treatment. We are going to use extensive simulation to evaluate the operating characteristics of our methods.^